L1CAM胞内区相互作用蛋白的筛选与鉴定

L1细胞粘附分子(L1cell adhesion molecular,L1CAM)属于神经细胞粘附分子,是属于免疫球蛋白超家族的Ⅰ型跨膜糖蛋白.L1主要在神经系统中表达,参与神经系统发育,学习记忆等重要过程作用.L1的胞内区可能参与信号转导,对于L1的功能非常重要,为探讨L1胞内区信号转导的分子机制,以L1胞内区为诱饵运用酵母双杂交技术在人脑cDNA文库中筛选其结合蛋白,挑选阳性克隆,进行DNA序列分析和同源检索,阳性克隆编码几个不同的蛋白质,其中一个候选蛋白为PAX6转录因子.为进一步验证L1胞内区和PAX6的相互作用,克隆其基因到表达质粒共转染COS-7细胞,免疫共沉淀证实了L1胞内区和PAX6的相互作用,提示L1胞内区可能参与转录调节,为深入探讨其功能提供了重要线索.     

Identification of the Ubiquitin-like Domain of Midnolin as a New Glucokinase Interaction Partner

Glucokinase acts as a glucose sensor in pancreatic beta cells. Its posttranslational regulation is important but not yet fully understood. Therefore, a pancreatic islet yeast two-hybrid library was produced and searched for glucokinase-binding proteins. A protein sequence containing a full-length ubiquitin-like domain was identified to interact with glucokinase. Mammalian two-hybrid and fluorescence resonance energy transfer analyses confirmed the interaction between glucokinase and the ubiquitin-like domain in insulin-secreting MIN6 cells and revealed the highest binding affinity at low glucose. Overexpression of parkin, an ubiquitin E3 ligase exhibiting an ubiquitin-like domain with high homology to the identified, diminished insulin secretion in MIN6 cells but had only some effect on glucokinase activity. Overexpression of the elucidated ubiquitin-like domain or midnolin, containing exactly this ubiquitin-like domain, significantly reduced both intrinsic glucokinase activity and glucose-induced insulin secretion. Midnolin has been to date classified as a nucleolar protein regulating mouse development. However, we could not confirm localization of midnolin in nucleoli. Fluorescence microscopy analyses revealed localization of midnolin in nucleus and cytoplasm and co-localization with glucokinase in pancreatic beta cells. In addition we could show that midnolin gene expression in pancreatic islets is up-regulated at low glucose and that the midnolin protein is highly expressed in pancreatic beta cells and also in liver, muscle, and brain of the adult mouse and cell lines of human and rat origin. Thus, the results of our study suggest that midnolin plays a role in cellular signaling of adult tissues and regulates glucokinase enzyme activity in pancreatic beta cells.     

Sequential Elution Interactome Analysis of the Mind Bomb 1 Ubiquitin Ligase Reveals a Novel Role in Dendritic Spine Outgrowth

The mind bomb 1 (Mib1) ubiquitin ligase is essential for controlling metazoan development by Notch signaling and possibly the Wnt pathway. It is also expressed in postmitotic neurons and regulates neuronal morphogenesis and synaptic activity by mechanisms that are largely unknown. We sought to comprehensively characterize the Mib1 interactome and study its potential function in neuron development utilizing a novel sequential elution strategy for affinity purification, in which Mib1 binding proteins were eluted under different stringency and then quantified by the isobaric labeling method. The strategy identified the Mib1 interactome with both deep coverage and the ability to distinguish high-affinity partners from low-affinity partners. A total of 817 proteins were identified during the Mib1 affinity purification, including 56 high-affinity partners and 335 low-affinity partners, whereas the remaining 426 proteins are likely copurified contaminants or extremely weak binding proteins. The analysis detected all previously known Mib1-interacting proteins and revealed a large number of novel components involved in Notch and Wnt pathways, endocytosis and vesicle transport, the ubiquitin-proteasome system, cellular morphogenesis, and synaptic activities. Immunofluorescence studies further showed colocalization of Mib1 with five selected proteins: the Usp9x (FAM) deubiquitinating enzyme, alpha-, beta-, and delta-catenins, and CDKL5. Mutations of CDKL5 are associated with early infantile epileptic encephalopathy-2 (EIEE2), a severe form of mental retardation. We found that the expression of Mib1 down-regulated the protein level of CDKL5 by ubiquitination, and antagonized CDKL5 function during the formation of dendritic spines. Thus, the sequential elution strategy enables biochemical characterization of protein interactomes; and Mib1 analysis provides a comprehensive interactome for investigating its role in signaling networks and neuronal development.Mind bomb 1 (Mib1)¹, an E3 ubiquitin ligase, is a critical regulator of metazoan development with a large, and ever expanding, number of functions through interactions with a variety of protein partners. Mib1 mutants were first found in zebrafish mutagenesis screens (1), in which the mutants had neurogenic defects, most notably supernumerary primary neurons, and additional deficits in the development of somites (2), ear (3), and vasculature (4). These phenotypes are predominantly the consequences of impaired Notch signaling, as Mib1 is an essential activator of Notch Delta/Serrate/lag-2 (DSL) ligands (1). Mib1 also controls the development of several other organ and tissue systems, including gastrointestinal tract (5), limb bud (6), and the immune system (7). Mib1 is highly conserved across species. For instance, zebrafish Mib1 protein is 68%, 94%, and 94% identical to its fly, mouse, and human orthologs, respectively (8). Moreover, Mib1 has a paralog (Mib2) that shares 38% identical protein sequence with Mib1 in mouse (9). Mib2 is only abundantly expressed in adult tissue, however, and thus does not function in early development. Consistently, Mib1 knockout in mice results in embryonic mortality (10), whereas Mib2 deletion has no obvious effect on mouse development (6).In addition to its role in cell fate determination during early development, Mib1 is also abundantly expressed in the adult brain (11) and plays an important role in neuronal morphogenesis (12). Neurons usually have two basic polarized structures, a single extended axon for sending signals and multiple branched dendrites (or more precisely, the somatodendritic compartment) for receiving signals. Many principle neurons in mammals further grow dendritic spines that are tiny protrusions extended from dendritic branches, creating local postsynaptic compartments for the formation of excitatory synapses. In these synapses, the postsynaptic density (PSD) is an electron-dense membrane thickening aligned with the presynaptic active zone at synaptic junctions. During neuronal morphogenesis, axonal growth and path finding (13), dendrite formation (14), dendritic spine assembly (15), and synaptogenesis (16) are independent but highly related processes controlled by genetic elements and environmental cues. Although dramatic progress has been made in identifying the signaling cascades responsible for these processes, large gaps still remain in the connection of individual signaling components as well as in the coordination of multiple pathways. Our previous proteomics analysis identified that Mib1 is highly enriched in the PSD fraction, and regulates neurite outgrowth in postmitotic neurons (12). Mib1 conditional knockout mouse studies suggest a role in long-term potentiation (LTP) and synaptic plasticity (11), and further intriguing actions of Mib1 continue to be discovered. Mib1 was found to mediate the degradation of survival motor neuron 1 (SMN1), which contributes to spinal muscular atrophy (17). Mib1 was reported to be essential for Wnt3A activation of beta-catenin signaling through the receptor RYK (18), and a recent yeast two-hybrid screen indicated that Mib1 interacts with 81 candidate proteins beyond the canonical Notch pathway (19). The ongoing identification of new Mib1 interaction partners and functions underscores the need to characterize the Mib1 interactome en masse with high confidence.The combination of affinity purification and liquid chromatography-tandem mass spectrometry (LC-MS/MS) has emerged as a powerful method for analyzing protein interaction networks. Technological advances in LC-MS/MS have continually increased the sensitivity of protein detection (20, 21), allowing for the analysis of complex samples (22). The primary advantage of this technique, however, has also proven to be its greatest weakness: without stringent washes and data filtering, a vast number of false positives are included in the resulting data sets (23). Methods such as tandem-affinity purification (24) have been developed to remove nonspecific contaminants, but two-step purification requires large quantities of starting materials and reduces sensitivity to loosely bound proteins. Removing contaminants by buffers containing high concentrations of salt and detergents can help limit false positives, but a delicate balance lies between rinsing contaminants and losing weakly bound but true interaction partners, and thus inflating false negative results. In addition, in vivo crosslinking and quantitative analysis are used to enhance the capture of transient interacting proteins (25, 26).To this end, we attempted to characterize the Mib1 interactome by combining glutathione S-transferase (GST) protein affinity purification and advanced quantitative mass spectrometry. In our sequential elution strategy, Mib1 interaction partners were bound to affinity resins coated with GST-Mib1 domains, then eluted in three sequential buffers of increasing stringency. Proteins in these three eluents were identified and quantified by an isobaric labeling Tandem Mass Tag (TMT) method (15). The elution profile of each protein reflected its binding affinity to the GST-Mib1 resins. The strategy not only provides high sensitivity to recover weakly bound partners, but also allows for the affinity-based classification of the interactome and the removal of contaminants. By this approach, we were able to recover 817 putative Mib1 binding partners in adult rat brain and accepted about half of the proteins with high confidence. This study also uncovered that Mib1 interacts with CDKL5, a protein kinase implicated in early infantile epileptic encephalopathy-2 (EIEE2), a severe form of epilepsy and mental retardation in females (28). We then found that Mib1 acts to down-regulate CDKL5 and inhibits its promotion of dendritic spine outgrowth.     

Identification of the Matriptase Second CUB Domain as the Secondary Site for Interaction with Hepatocyte Growth Factor Activator Inhibitor Type-1

Matriptase is a type II transmembrane serine protease comprising 855 amino acid residues. The extracellular region of matriptase comprises a noncatalytic stem domain (containing two tandem repeats of complement proteases C1r/C1s-urchin embryonic growth factor-bone morphogenetic protein (CUB) domain) and a catalytic serine protease domain. The stem domain of matriptase contains site(s) for facilitating the interaction of this protease with the endogenous inhibitor, hepatocyte growth factor activator inhibitor type-1 (HAI-1). The present study aimed to identify these site(s). Analyses using a secreted variant of recombinant matriptase comprising the entire extracellular domain (MAT), its truncated variants, and a recombinant HAI-1 variant with an entire extracellular domain (HAI-1–58K) revealed that the second CUB domain (CUB domain II, Cys³⁴⁰–Pro⁴⁵²) likely contains the site(s) of interest. We also found that MAT undergoes cleavage between Lys³⁷⁹ and Val³⁸⁰ within CUB domain II and that the C-terminal residues after Val³⁸⁰ are responsible for facilitating the interaction with HAI-1–58K. A synthetic peptide corresponding to Val³⁸⁰–Asp³⁹⁰ markedly increased the matriptase-inhibiting activity of HAI-1–58K, whereas the peptides corresponding to Val³⁸⁰–Val³⁸⁹ and Phe³⁸²–Asp³⁹⁰ had no effect. HAI-1–58K precipitated with immobilized streptavidin resins to which a synthetic peptide Val³⁸⁰–Pro³⁹² with a biotinylated lysine residue at its C terminus was bound, suggesting direct interaction between CUB domain II and HAI-1. These results led to the identification of the matriptase CUB domain II, which facilitates the primary inhibitory interaction between this protease and HAI-1.     

斑马鱼胚胎中受Nodal信号调控基因的鉴定

Nodal信号在脊椎动物胚胎发育的中内胚层诱导、左右不对称性的建立、神经外胚层沿前后轴线的分化等方面起着重要的作用.为鉴定受Nodal信号调控的基因,特别是那些转录因子基因,通过将来自squint过量表达、缺失Nodal信号的MZoep突变体或野生型30%外包期胚胎的RNA与Affymetrix斑马鱼寡核苷酸芯片杂交.发现与野生型样本相比,在squint过量表达的样本中,265个转录本的表达显著增强(log2ratio>1),111个转录本的表达显著减弱(log2ratio<-1);在MZoep样本中,表达显著增强的(log2ratio>1)转录本有1495个,表达显著减弱(log2ratio<-1)的有550个.squint过量表达使26个转录因子基因的表达增强,11个转录因子基因的表达减弱;另一方面,MZoep突变体中表达增强的转录因子基因为69个,表达减弱的转录因子基因为30个.这些结果为进一步研究Nodal信号的转导机理和生物学功能提供了有益的数据.     

以透明脑,观澄明心——斑马鱼神经功能研究进展

斑马鱼是一种相对新颖的模式脊椎动物,具有脊椎动物保守的神经系统构造和丰富的行为模式.近年来随着在体电生理、光学成像、遗传工程等方法的建立和完善,幼龄斑马鱼因其脑部透明、结构简单的特点,日益成为从突触、神经元、环路到行为等多层次,在全脑尺度上探究神经系统功能机制的理想动物模型.本文综述了近年来利用斑马鱼在感觉信息处理、运动控制、学习与神经可塑性等方向上所取得的重要研究进展,并对新技术的开发提出了展望.随着研究思路的深化和实验手段的推陈出新,斑马鱼模式动物必将成为探索脑工作原理之利器,为神经科学研究带来更多的突破.     

Actinin-associated LIM Protein: Identification of a Domain Interaction between PDZ and Spectrin-like Repeat Motifs

PDZ motifs are protein–protein interaction domains that often bind to COOH-terminal peptide sequences. The two PDZ proteins characterized in skeletal muscle, syntrophin and neuronal nitric oxide synthase, occur in the dystrophin complex, suggesting a role for PDZ proteins in muscular dystrophy. Here, we identify actinin-associated LIM protein (ALP), a novel protein in skeletal muscle that contains an NH₂-terminal PDZ domain and a COOH-terminal LIM motif. ALP is expressed at high levels only in differentiated skeletal muscle, while an alternatively spliced form occurs at low levels in the heart. ALP is not a component of the dystrophin complex, but occurs in association with α-actinin-2 at the Z lines of myofibers. Biochemical and yeast two-hybrid analyses demonstrate that the PDZ domain of ALP binds to the spectrin-like motifs of α-actinin-2, defining a new mode for PDZ domain interactions. Fine genetic mapping studies demonstrate that ALP occurs on chromosome 4q35, near the heterochromatic locus that is mutated in fascioscapulohumeral muscular dystrophy.     

Role of Phosphotyrosine Interaction Domain Containing 1 in Porcine Intramuscular Preadipocyte Proliferation and Differentiation

Phosphotyrosine interaction domain containing 1 (PID1), a recently identified gene involved in obesity-associated insulin resistance, plays an important role in fat deposition. However, its effect on porcine intramuscular preadipocyte proliferation and differentiation remains poorly understood. In this study, the plasmid pcDNA3.1(+)-pPID1 was transfected into porcine intramuscular preadipocytes with Lipofectamine 3000 reagent to over-express porcine PID1 (pPID1). Over-expression of pPID1 significantly promoted porcine intramuscular preadipocyte proliferation. Expression of pPID1 mRNA was significantly increased upon porcine intramuscular preadipocyte differentiation. Indirect fluorescent immunocytochemistry demonstrated that pPID1 protein was localized predominantly in the nucleus of porcine intramuscular preadipocyte. The mRNA levels of peroxisome proliferators-activated receptor γ, CCAAT/enhancer binding protein α and lipoprotein lipase were significantly increased by pPID1 over-expression. Over-expression of pPID1 also led to an increase in lipid accumulation which was detected by Oil Red O staining, and significantly increased the intramuscular triacylglycerol content. These results indicate that pPID1 may play a role in enhancing porcine intramuscular preadipocyte proliferation and differentiation.     

Identification and Expression of the Family of Classical Protein-Tyrosine Phosphatases in Zebrafish

Protein-tyrosine phosphatases (PTPs) have an important role in cell survival, differentiation, proliferation, migration and other cellular processes in conjunction with protein-tyrosine kinases. Still relatively little is known about the function of PTPs in vivo. We set out to systematically identify all classical PTPs in the zebrafish genome and characterize their expression patterns during zebrafish development. We identified 48 PTP genes in the zebrafish genome by BLASTing of human PTP sequences. We verified all in silico hits by sequencing and established the spatio-temporal expression patterns of all PTPs by in situ hybridization of zebrafish embryos at six distinct developmental stages. The zebrafish genome encodes 48 PTP genes. 14 human orthologs are duplicated in the zebrafish genome and 3 human orthologs were not identified. Based on sequence conservation, most zebrafish orthologues of human PTP genes were readily assigned. Interestingly, the duplicated form of ptpn23, a catalytically inactive PTP, has lost its PTP domain, indicating that PTP activity is not required for its function, or that ptpn23b has lost its PTP domain in the course of evolution. All 48 PTPs are expressed in zebrafish embryos. Most PTPs are maternally provided and are broadly expressed early on. PTP expression becomes progressively restricted during development. Interestingly, some duplicated genes retained their expression pattern, whereas expression of other duplicated genes was distinct or even mutually exclusive, suggesting that the function of the latter PTPs has diverged. In conclusion, we have identified all members of the family of classical PTPs in the zebrafish genome and established their expression patterns. This is the first time the expression patterns of all members of the large family of PTP genes have been established in a vertebrate. Our results provide the first step towards elucidation of the function of the family of classical PTPs.     

斑马鱼心肌特异性启动子的克隆及其功能鉴定*

目的:探讨心室肌球蛋白重链(vmhc)基因启动子的心肌组织特异性.方法:利用PCR技术从斑马鱼基因组中克隆了vmhc编码区5’上游大小为1952bp的调控区域,应用酶切连接方法将vmhc启动子插入pGEFP-N1质粒,成功构建pEGFP-vmhc重组载体.再应用高保真DNA聚合酶PCR扩增包含vmhc启动子序列,增强型绿色荧光蛋白(EGFP)基因序列及3'UTR序列的基因片段,经过纯化后通过显微注射将vmhc-EGFP基因片段导入斑马鱼受精卵中.结果:注射后的斑马鱼心脏中出现绿色荧光,而其他部位无荧光出现.结论:vmhc启动子能够正确有效地驱动外源基因在斑马鱼心脏中特异表达,适合应用于心血管疾病的基因功能研究,基因靶向治疗等.     

DLC1 Activation Requires Lipid Interaction through a Polybasic Region Preceding the RhoGAP Domain

Deleted in Liver Cancer 1 (DLC1) is a GTPase-activating protein (GAP) with specificity for RhoA, RhoB, and RhoC that is frequently deleted in various tumor types. By inactivating these small GTPases, DLC1 controls actin cytoskeletal remodeling and biological processes such as cell migration and proliferation. Here we provide evidence that DLC1 binds to phosphatidylinositol-4,5-bisphosphate (PI(4,5)P₂) through a previously unrecognized polybasic region (PBR) adjacent to its RhoGAP domain. Importantly, PI(4,5)P₂-containing membranes are shown to stimulate DLC1 GAP activity in vitro. In living cells, a DLC1 mutant lacking an intact PBR inactivated Rho signaling less efficiently and was severely compromised in suppressing cell spreading, directed migration, and proliferation. We therefore propose that PI(4,5)P₂ is an important cofactor in DLC1 regulation in vivo and that the PBR is essential for the cellular functions of the protein.     

Identification and Characterization of the Interaction between ZmSBEIIb and ZmPAD1 in Maize

Russian Journal of Plant Physiology - The starch branching enzymes (SBEs) play critical roles in forming branched structures (α-1,6-glycosidic linkages) of starch molecules in maize (Zea mays...     

解纤维梭菌纤维小体黏附域与锚定域相互作用的差异性

黏附域(cohesin)与锚定域(dockerin)的相互作用是纤维素酶复合体-纤维小体(cellulosome)组装的基础,该作用是自然界已知最强的相互作用力之一。为解析纤维小体的装配机制,本研究以解纤维梭菌(Ruminiclostridium cellulolyticum)纤维小体为研究对象,通过Pull-down和等温滴定量热(ITC)的方法,分析并比较不同簇的3个黏附域与7个锚定域之间的相互作用。结果表明,不同簇黏附域与锚定域的相互作用具有显著差异。其中,Coh1与Doc-0729的相互作用最强,K_a为10⁸ M^-1,Coh7与Doc-0729、0931作用力强,K_a为10⁷ M^-1,而Coh8与Doc-0931、1656、0752作用强,K_a也达到10⁷ M^-1。总之,Doc-0729、0931、1656与3个Coh的结合力均较高。本研究揭示了纤维小体黏附域与锚定域的组装具有偏爱性...     

The I Domain is Essential for Echovirus 1 Interaction with VLA-2

VLA-2, the α2β1 integrin, mediates cell adhesion to collagen and laminin, and is the receptor for the human pathogen echovirus 1. Because of its similarity to domains present in other proteins that interact with collagen, a 191 amino acid region within the α2 subunit (the I domain) has been proposed as a potential site for ligand interactions. Although the α2 subunits of human and murine VLA-2 are 84% identical, human α2 promotes virus binding whereas murine α2 does not. We used murine/human chimeric α2 molecules to identify regions of the human molecule essential for virus binding. Virus bound efficiently to a chimeric protein in which the human I domain was inserted into murine α2, indicating that the human I domain is responsible for specific virus interactions. Monoclonal antibodies that inhibited virus attachment all recognized epitopes within the human I do-main, further suggesting that virus interacts with this portion of the molecule. Similarly, antibodies that prevented VLA-2-mediated cell adhesion to collagen also mapped to the I domain. These results indicate that the I domain plays a role in VLA-2 interactions both with virus and with extracellular matrix ligands.